DRYAD_DATASET_GLADIEUX

DRYAD_DATASET_GLADIEU

Summary of K2P distances for increasing taxonomic levels. Data are from 2276 sequences from 668 species and 265 genera (<i>SI</i> Appendix S2). Comparisons within species based on the 514 species with <i>N</i>>1.

<p>Summary of K2P distances for increasing taxonomic levels. Data are from 2276 sequences from 668 species and 265 genera (<i>SI</i> Appendix S2). Comparisons within species based on the 514 species with <i>N</i>>1.</p

Summary of the predictions from the Centre-of-Overlap and Centre-of-Origin hypotheses.

<p>Summary of the predictions from the Centre-of-Overlap and Centre-of-Origin hypotheses.</p

Map of the sampling localities and position of the Indo-Malay-Philippines Archipelago (IMPA) peak of diversity (derived from [<b>17</b>]).

<p>Map of the sampling localities and position of the Indo-Malay-Philippines Archipelago (IMPA) peak of diversity (derived from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028987#pone.0028987-Bellwood2" target="_blank">[<b>17</b>]</a>).</p

Plot describing the discriminatory power (expressed as G/N, the ratio between the number of haplotypes and the number of strains) in relation to the number of TR loci assayed.

<p>Black dashes represent the range of G/N ratios. Red dashes indicate 2.5 and 97.5% quantiles. Red dots indicate the median G/N values.</p

Minisatellite and primer description, amplification conditions, number of alleles and Nei's genetic diversity (H_T) for 31 minisatellite markers tested on strains of <i>Xanthomonas citri</i> pv. <i>citri</i> from a worldwide strain collection.

a<p>Italicized loci are proposed for routine analyses (MLVA-12).</p>b<p>As annotated in the IAPAR 306 genome; -: intergenic; NA: not appropriate.</p

Genetic and pathological diversity and geographical origin of <i>Xanthomonas citri</i> pv. <i>citri</i> strains within the four DAPC clusters.

a<p>N number of isolates; N_H number of haplotypes; H_E within-cluster Nei's genetic diversity; NA not appropriate.</p>b<p>Subclustering was performed based on clonal complexes identified by goeBURST for DAPC clusters containing at least ten haplotypes (see materials and methods) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098129#pone.0098129-Francisco1" target="_blank">[49]</a>.</p>c<p>A single pathotype A* strain (JF90-8 from Oman) was assigned to DAPC cluster 2.</p

Categorical minimum spanning tree from MLVA-31 data (129 strains –72 haplotypes) representing the genetic diversity within a worldwide strain collection of <i>Xanthomonas citri</i> pv. <i>citri</i> in relation with its pathological diversity.

<p>Dot diameter and color are representative of the number of strains per haplotype and pathotype, respectively (red: pathotype A; blue: pathotype A*; green: pathotype A^w). Numbers in dots are for haplotype numbers. Numbers along the links indicate the number of polymorphic TR loci distinguishing haplotypes. Haplotypes in a same colored ellipse were assigned to a same genetic cluster by Discriminant Analysis of Principal Components. Dashed ellipses indicate subclusters, as defined by goeBURST <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098129#pone.0098129-Francisco1" target="_blank">[49]</a>.</p

Circular representation of the genome sequence of <i>Xam</i> CIO151.

<p>From outside to inside: first circle in blue indicates CDS predicted in the positive strands for the scaffolds classified as probable chromosomal regions. Second circle in red indicates the CDS predicted in the negative strand. Red spots in the black third circle indicate the region identified with atypical nucleotide composition. The fourth circle indicates the deviation pattern from the average G+C content. Inner circle shows GC skew values, positive values are shown in purple and negative values are shown in orange. Numbers correspond to scaffold IDs.</p

Putative pathogenicity elements identified in the genome of <i>Xam</i> CIO151.

1<p>Number indicates CDS identified by key word searches in iANT.</p